Geographic and species association of hepatitis B virus genotypes in non-human primates

AbstractInfection with hepatitis B virus (HBV) has been detected in human populations thoughout the world, as well as in a number of ape species (Pan troglodytes, Gorilla gorilla, gibbons [Nomascus and Hylobates species] and Pongo pygmaeus). To investigate the distribution of naturally occurring HBV infection in these species and other African Old World monkey species (Cercopithecidae), we screened 137 plasma samples from mainly wild caught animals by polymerase chain reaction (PCR) using several of highly conserved primers from the HB surface (HBs) gene, and for HBs antigen (HBsAg) by ELISA. None of the 93 Cercopithecidae screened (6 species) showed PCR or serology evidence for HBV infection; in contrast 2 from 8 chimpanzees and 5 from 22 gibbons were PCR-positive with each set of primers.Complete genome sequences from each of the positive apes were obtained and compared with all previously published complete and surface gene sequences. This extended phylogenetic analysis indicated that HBV variants from orangutans were interspersed by with HBV variants from southerly distributed gibbon species (H. agilis and H. moloch) occupying overlapping or adjacent habitat ranges with orangutans; in contrast, HBV variants from gibbon species in mainland Asia were phylogenetically distinct. A geographical rather than (sub)species association of HBV would account for the distribution of HBV variants in different subspecies of chimpanzees in Africa, and explain the inlier position of the previously described lowland gorilla sequence in the chimpanzee clade. These new findings have a number of implication for understanding the origins and epidemiology of HBV infection in non-human primates

Supernova Neutrinos, Neutrino Oscillations, and the Mass of the Progenitor Star

We investigate the initial progenitor mass dependence of the early-phase neutrino signal from supernovae taking neutrino oscillations into account. The early-phase analysis has advantages in that it is not affected by the time evolution of the density structure of the star due to shock propagation or whether the remnant is a neutron star or a black hole. The initial mass affects the evolution of the massive star and its presupernova structure, which is important for two reasons when considering the neutrino signal. First, the density profile of the mantle affects the dynamics of neutrino oscillation in supernova. Second, the final iron core structure determines the features of the neutrino burst, i.e., the luminosity and the average energy. We find that both effects are rather small. This is desirable when we try to extract information on neutrino parameters from future supernova-neutrino observations. Although the uncertainty due to the progenitor mass is not small for intermediate $\theta_{13}$ ($10^{-5} \lesssim \sin^{2}{2 \theta_{13}} \lesssim 10^{-3}$), we can, nevertheless, determine the character of the mass hierarchy and whether $\theta_{13}$ is very large or very small.Comment: 8 pages, 15 figure

Effects of Neutrino Oscillation on the Supernova Neutrino Spectrum

The effects of three-flavor neutrino oscillation on the supernova neutrino spectrum are studied. We calculate the expected event rate and energy spectra, and their time evolution at the Superkamiokande (SK) and the Sudbury Neutrino Observatory (SNO), by using a realistic neutrino burst model based on numerical simulations of supernova explosions. We also employ a realistic density profile based on a presupernova model for the calculation of neutrino conversion probability in supernova envelopes. These realistic models and numerical calculations allow us to quantitatively estimate the effects of neutrino oscillation in a more realistic way than previous studies. We then found that the degeneracy of the solutions of the solar neutrino problem can be broken by the combination of the SK and SNO detections of a future Galactic supernova.Comment: 10 pages, 14 figures, corrected versio

Dynamics and stress in gravity driven granular flow

We study, using simulations, the steady-state flow of dry sand driven by gravity in two-dimensions. An investigation of the microscopic grain dynamics reveals that grains remain separated but with a power-law distribution of distances and times between collisions. While there are large random grain velocities, many of these fluctuations are correlated across the system and local rearrangements are very slow. Stresses in the system are almost entirely transfered by collisions and the structure of the stress tensor comes almost entirely from a bias in the directions in which collisions occur.Comment: 4 pages, 3 eps figures, RevTe

Reaction rate for two--neutron capture by 4^4He

Recent investigations suggest that the neutrino--heated hot bubble between the nascent neutron star and the overlying stellar mantle of a type--II supernova may be the site of the r--process. In the preceding $\alpha$--process building up the elements to $A \approx 100$, the $^4$He(2n,$\gamma$)$^6$He-- and $^6$He($\alpha$,n)$^9$Be--reactions bridging the instability gap at $A=5$ and $A=8$ could be of relevance. We suggest a mechanism for $^4$He(2n,$\gamma$)$^6$He and calculate the reaction rate within the $\alpha$+n+n approach. The value obtained is about a factor 1.6 smaller than the one obtained recently in the simpler direct--capture model, but is at least three order of magnitude enhanced compared to the previously adopted value. Our calculation confirms the result of the direct--capture calculation that under representative conditions in the $\alpha$--process the reaction path proceeding through $^6$He is negligible compared to $^4$He($\alpha$n,$\gamma$)$^9$Be.Comment: 13 pages, 4 postscript figures, to appear in "Zeitschrift f. Physik A", changed internet address and filename, the uuencoded postscript file including the figures is available at ftp://is1.kph.tuwien.ac.at/pub/ohu/twoneutron.u

Terminal restriction fragment length polimorphism (T-RFLP) : una herramienta útil para valorar la dinámica y la diversidad de la población microbiana en aves y cerdos

El ecosistema intestinal es un medio complejo y dinámico que puede verse afectado puntualmente por numerosos factores propios del individuo pero también por numerosos factores ambientales o externos (como puede ser la dieta). La necesidad de conocer de una forma rápida y reproducible cómo es la dinámica de la población bacteriana, así como su estructura está siendo posible gracias al desarrollo de técnicas moleculares aplicadas como DGGE (Denaturing Gradient Gel Electrophoresis)1, TGGE (Temperatura Gradient Gel Electrophoresis)2, SSCP (Single Strand Conformation Polimorphism)3 y T-RFLP (Terminal Restriction Fragment Length Polimorphism)4. Estas técnicas moleculares aprovechan la característica de universalidad del gen que codifica para el 16S ARNr, presente en prácticamente la totalidad de las especies bacterianas. La presencia de secuencias altamente conservadas hace posible el diseño de primers o cebadores que permitan la amplificación mediante PCR del total de la población bacteriana de la muestra. Son las regiones variables (polimórficas) del gen que codifica el 16S ARNr las que se aprovechan para la diferenciación. En el T-RFLP, estas diferencias entre especies o géneros bacterianos se ponen de manifiesto tras la digestión con endonucleasas de restricción del producto de PCR marcado. Únicamente el fragmento del extremo terminal será visible por electroforesis capilar gracias al mareaje fluorescente de uno de los cebadores. El perfil que se genera (electroferograma) nos permite obtener información del número de fragmentos (riqueza), de su tamaño en pares de bases (bp) (para una posible inferencia de la especie bacteriana presente) y de su altura (lo que puede orientar sobre la importancia de un determinado grupo bacteriano dentro de una muestra), siempre sin olvidar las desviaciones inherentes propias de la PCR. Es posible también calcular la frecuencia de detección de un determinado pico (especie) respecto al total de muestras así como construir con ayuda de programas informáticos matrices de similitud o dendogramas. Empleando herramientas disponibles en la red como: TAP-tRFLP del software Ribosomal Database Project II o ISPaR del software MiCA (Microbial Community Analysis) es posible hacer una asignación teórica de la especie o género bacteriano a cada uno de los picos en base a las secuencias depositadas por otros autores. Sin embargo un mismo pico puede tener su origen en distintas especies. Disponer alternativamente de secuencias propias obtenidas tras la clonación del 16S ARN de muestras de nuestros animales nos permite hacer una asignación teórica más firme, considerando únicamente aquellas especies mayoritarias encontradas

Dynamics of microbial cecal lumen ecosystem of broiler chickens with age measured by Terminal Restriction Fragment Length Polymorphism (t-RFLP)

Nowadays, it is known that intestinal microflora of broiler chickens plays an important role for growth performance and health. However, there is still a limited knowledge about the process of colonization of the chick gut

Two-spinon dynamic structure factor of the one-dimensional S=1/2 Heisenberg antiferromagnet

The exact expression derived by Bougourzi, Couture, and Kacir for the 2-spinon contribution to the dynamic spin structure factor $S_{zz}(q,\omega)$ of he one-dimensional $S$=1/2 Heisenberg antiferromagnet at $T=0$ is evaluated for direct comparison with finite-chain transition rates ($N\leq 28$) and an approximate analytical result previously inferred from finite-$N$ data, sum rules, and Bethe-ansatz calculations. The 2-spinon excitations account for 72.89% of the total intensity in $S_{zz}(q,\omega)$. The singularity structure of the exact result is determined analytically and its spectral-weight distribution evaluated numerically over the entire range of the 2-spinon continuum. The leading singularities of the frequency-dependent spin autocorrelation function, static spin structure factor, and $q$-dependent susceptibility are determined via sum rules.Comment: 6 pages (RevTex) and 5 figures (Postscript

Test of Replica Theory: Thermodynamics of 2D Model Systems with Quenched Disorder

We study the statistics of thermodynamic quantities in two related systems with quenched disorder: A (1+1)-dimensional planar lattice of elastic lines in a random potential and the 2-dimensional random bond dimer model. The first system is examined by a replica-symmetric Bethe ansatz (RBA) while the latter is studied numerically by a polynomial algorithm which circumvents slow glassy dynamics. We establish a mapping of the two models which allows for a detailed comparison of RBA predictions and simulations. Over a wide range of disorder strength, the effective lattice stiffness and cumulants of various thermodynamic quantities in both approaches are found to agree excellently. Our comparison provides, for the first time, a detailed quantitative confirmation of the replica approach and renders the planar line lattice a unique testing ground for concepts in random systems.Comment: 16 pages, 14 figure

Star and Planet Formation with ALMA: an Overview

Submillimeter observations with ALMA will be the essential next step in our understanding of how stars and planets form. Key projects range from detailed imaging of the collapse of pre-stellar cores and measuring the accretion rate of matter onto deeply embedded protostars, to unravelling the chemistry and dynamics of high-mass star-forming clusters and high-spatial resolution studies of protoplanetary disks down to the 1 AU scale.Comment: Invited review, 8 pages, 5 figures; to appear in the proceedings of "Science with ALMA: a New Era for Astrophysics". Astrophysics & Space Science, in pres